git annex restage
Since getting or dropping an unlocked file modifies the file in the work tree, git needs to be told that the modification does not change the content that it has recorded (the annex pointer). Restaging the file accomplishes that.
You do not normally need to run this command, because usually git-annex is able to restage unlocked files itself. There are some situations where git-annex needs to restage a file, but the git index is locked, and so it cannot. It will then display a warning suggesting you run this command.
It's safe to run this command even after you have made a modification to an unlocked file.
Joey Hess <firstname.lastname@example.org>